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Van A. Ngo, Ph.D. - Publications

Affiliations: 
2014 Physics University of Southern California, Los Angeles, CA, United States 
Area:
Theory Physics, General Biophysics
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36 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Kudaibergenova M, Guo J, Khan HM, Lees-Miller J, Mousaei M, Miranda W, Ngo VA, Noskov SY, Tieleman DP, Duff HJ. The voltage-sensing domain of a hERG1 mutant is a cation-selective channel. Biophysical Journal. 121: 4585-4599. PMID 36815709 DOI: 10.1016/j.bpj.2022.10.032  0.349
2022 Ngo VA, Queralt-Martín M, Khan F, Bergdoll L, Abramson J, Bezrukov SM, Rostovtseva TK, Hoogerheide DP, Noskov SY. The Single Residue K12 Governs the Exceptional Voltage Sensitivity of Mitochondrial Voltage-Dependent Anion Channel Gating. Journal of the American Chemical Society. 144: 14564-14577. PMID 35925797 DOI: 10.1021/jacs.2c03316  0.34
2021 Ngo V, Li H, MacKerell AD, Allen TW, Roux B, Noskov S. Polarization Effects in Water-Mediated Selective Cation Transport across a Narrow Transmembrane Channel. Journal of Chemical Theory and Computation. PMID 33539082 DOI: 10.1021/acs.jctc.0c00968  0.456
2020 Zhang Y, Haider K, Kaur D, Ngo VA, Cai X, Mao J, Khaniya U, Zhu X, Noskov S, Lazaridis T, Gunner MR. Characterizing the water wire in the Gramicidin channel found by Monte Carlo sampling using continuum electrostatics and in molecular dynamics trajectories with conventional or polarizable force fields Journal of Theoretical and Computational Chemistry. 2042001. DOI: 10.1142/S0219633620420018  0.374
2020 Queralt-Martin M, Ngo VA, Bergdoll LA, Abramson J, Hoogerheide DP, Rostovtseva TK, Bezrukov SM, Noskov SY. Solving the Gating Mechanism of the Mitochondrial β-Barrel Metabolite Channel VDAC Biophysical Journal. 118: 269a. DOI: 10.1016/J.Bpj.2019.11.1553  0.329
2019 Wang Y, Finol-Urdaneta RK, Ngo VA, French RJ, Noskov SY. Author Correction: Bases of Bacterial Sodium Channel Selectivity Among Organic Cations. Scientific Reports. 9: 18992. PMID 31813931 DOI: 10.1038/S41598-019-55306-4  0.365
2019 Nguyen TH, Ngo V, Castro Zerba JP, Noskov S, Minh DDL. Nonequilibrium path-ensemble averages for symmetric protocols. The Journal of Chemical Physics. 151: 194103. PMID 31757156 DOI: 10.1063/1.5121306  0.332
2019 Wang Y, Finol-Urdaneta RK, Ngo VA, French RJ, Noskov SY. Bases of Bacterial Sodium Channel Selectivity Among Organic Cations. Scientific Reports. 9: 15260. PMID 31649292 DOI: 10.1038/S41598-019-51605-Y  0.521
2019 Amin KS, Rostovtseva TK, Bezrukov SM, Noskov SY, Ngo V. State-Dependence of Ion and ATP Transport in VDAC1 Protein Investigated with GCMC/BD Simulations Biophysical Journal. 116. DOI: 10.1016/J.Bpj.2018.11.2152  0.4
2018 Miranda WE, Ngo VA, Wang R, Zhang L, Chen SRW, Noskov SY. Molecular Mechanism of Conductance Enhancement in Narrow Cation-Selective Membrane Channels. The Journal of Physical Chemistry Letters. 3497-3502. PMID 29886737 DOI: 10.1021/Acs.Jpclett.8B01005  0.489
2018 Farley RA, Holzmann S, Kopp C, Shi Y, Wang Y, Noskov S, Ngo VA. Nonequilibrium Molecular Dynamics (MD) Simulations of Multi-ion Permeation in KcsA Biophysical Journal. 114: 133a. DOI: 10.1016/J.Bpj.2017.11.753  0.431
2018 Miranda WE, Ngo VA, Chen SW, Noskov SY. Understanding the Molecular Mechanism of Cation Permeation in the Cardiac Ryanodine Receptor (RyR2) Channel using Computational Electrophysiology Biophysical Journal. 114: 115a. DOI: 10.1016/J.Bpj.2017.11.665  0.366
2018 Ngo V, Rostovtseva TK, Bezrukov SM, Noskov SY. Revealing Molecular Coupling between Anion Selectivity and Structural Transitions in Voltage-Dependent Anion Channel (VDAC) Biophysical Journal. 114. DOI: 10.1016/J.Bpj.2017.11.1714  0.397
2017 Miranda WE, Ngo VA, Perissinotti LL, Noskov SY. Computational Membrane Biophysics: From Ion Channels Interactions with Drugs to Cellular Function. Biochimica Et Biophysica Acta. PMID 28847523 DOI: 10.1016/J.Bbapap.2017.08.008  0.49
2017 Ngo VA, Perissinotti LL, Miranda W, Chen SRW, Noskov SY. Mapping Ryanodine Binding Sites in the Pore Cavity of Ryanodine Receptors. Biophysical Journal. 112: 1645-1653. PMID 28445755 DOI: 10.1016/J.Bpj.2017.03.014  0.316
2017 Zhekova HR, Ngo V, Silva MCd, Salahub D, Noskov S. Selective ion binding and transport by membrane proteins – A computational perspective Coordination Chemistry Reviews. 345: 108-136. DOI: 10.1016/J.Ccr.2017.03.019  0.463
2017 Ngo V, Wang Y, Noskov S. Unconventional Ion-Permeation Pathways in NaV Ab and Cav Ab Channels from Molecular Simulations with Polarizable Force-Fields Biophysical Journal. 112: 13a. DOI: 10.1016/J.Bpj.2016.11.105  0.586
2016 Miranda WE, Ngo VA, Valiente PA, Noskov SY. Improved QM/MM Linear Interaction Energy Model for Substrate Recognition in Zinc-Containing Metalloenzymes. The Journal of Physical Chemistry. B. PMID 27448039 DOI: 10.1021/Acs.Jpcb.6B05628  0.303
2016 Ngo VA, Kim I, Allen TW, Noskov SY. Estimation of Potentials of Mean Force from Non-Equilibrium Pulling Simulations Using Both Minh-Adib Estimator and Weighted Histogram Analysis Method. Journal of Chemical Theory and Computation. PMID 26799775 DOI: 10.1021/Acs.Jctc.5B01050  0.37
2016 Ngo V, Wang Y, Haas S, Noskov SY, Farley RA. K+ Block Is the Mechanism of Functional Asymmetry in Bacterial Nav Channels. Plos Computational Biology. 12: e1004482. PMID 26727271 DOI: 10.1371/Journal.Pcbi.1004482  0.686
2016 Ngo V, Noskov SY. A Trio of Cations in Gramicidin a Channel: Importance of Quantum Effects to Describe Ion Selectivity of K+ and Na+, and Proton Transfer Biophysical Journal. 110: 177a. DOI: 10.1016/J.Bpj.2015.11.989  0.55
2016 Farley RA, Shi Y, Wang Y, Ngo V, Noskov S. Molecular Dynamics Simulations of Mutant K Channels Involved in Severe Early Onset Epilepsy Biophysical Journal. 110: 449a. DOI: 10.1016/J.Bpj.2015.11.2411  0.513
2015 Ngo V, da Silva MC, Kubillus M, Li H, Roux B, Elstner M, Cui Q, Salahub DR, Noskov SY. Quantum Effects in Cation Interactions with First and Second Coordination Shell Ligands in Metalloproteins. Journal of Chemical Theory and Computation. 11: 4992-5001. PMID 26574284 DOI: 10.1021/Acs.Jctc.5B00524  0.396
2015 Li H, Ngo V, Da Silva MC, Salahub DR, Callahan K, Roux B, Noskov SY. Representation of Ion-Protein Interactions Using the Drude Polarizable Force-Field. The Journal of Physical Chemistry. B. 119: 9401-16. PMID 25578354 DOI: 10.1021/Jp510560K  0.458
2015 Ngo V, Wang Y, Noskov S, Haas S, Farley RA. Molecular Dynamics Simulations Describe the Mechanism of K Block in Bacterial Nav Channels Biophysical Journal. 108: 574a-575a. DOI: 10.1016/J.Bpj.2014.11.3142  0.663
2014 Ngo V, Stefanovski D, Haas S, Farley RA. Non-equilibrium dynamics contribute to ion selectivity in the KcsA channel. Plos One. 9: e86079. PMID 24465882 DOI: 10.1371/Journal.Pone.0086079  0.676
2014 Ngo VA, Di Felice R, Haas S. Is the G-quadruplex an effective nanoconductor for ions? The Journal of Physical Chemistry. B. 118: 864-72. PMID 24397412 DOI: 10.1021/Jp408071H  0.659
2014 Ngo V, Stefanovski D, Haas S, Farley RA. Z-Coordinates (Å) for Stable Positions for Na + and K + Ions After Each Pulling Step (Δλ = 1 Å). Plos One. DOI: 10.1371/Journal.Pone.0086079.T001  0.579
2014 Ngo V, Stefanovski D, Haas S, Farley RA. Calculated values of conductance (G) for a K + ion pulled through the KcsA channel using a step-wise pulling protocol. Plos One. DOI: 10.1371/Journal.Pone.0086079.G007  0.621
2014 Ngo V, Stefanovski D, Haas S, Farley RA. Free energy profiles for Na+ and K+ ions in the KcsA channel. Plos One. DOI: 10.1371/Journal.Pone.0086079.G002  0.656
2014 Ngo V, Wu H, Haas S, Farley R. Mechanism of Non-Selectivity in NAK Channel Biophysical Journal. 106: 558. DOI: 10.1016/J.Bpj.2013.11.3103  0.634
2014 Tabbakhian M, Ngo V, Haas S, Farley R. Amino Acid Substitutions for T75 in KCSA Alter Ion Selectivity Biophysical Journal. 106: 5-9. DOI: 10.1016/J.Bpj.2013.11.3004  0.663
2013 Ngo V, Stefanovski D, Farley R, Haas S. Thermal Effects and Free-Energy Barrier Differences in the Ion Selectivity Mechanism of KcsA Biophysical Journal. 104: 1-8. DOI: 10.1016/J.Bpj.2012.11.736  0.624
2012 Ngo VA, Haas S. Demonstration of Jarzynski's equality in open quantum systems using a stepwise pulling protocol. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 86: 031127. PMID 23030886 DOI: 10.1103/Physreve.86.031127  0.448
2012 Ngo VA. Parallel-pulling protocol for free-energy evaluation. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 85: 036702. PMID 22587204 DOI: 10.1103/Physreve.85.036702  0.31
2012 Ngo VA, Kalia RK, Nakano A, Vashishta P. Supercrystals of DNA-functionalized gold nanoparticles: A million-atom molecular dynamics simulation study Journal of Physical Chemistry C. 116: 19579-19585. DOI: 10.1021/Jp306133V  0.38
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